Fig. 2

Identifying host subpopulations in mouse macrophages exposed to Salmonella. a Bone marrow-derived macrophages, exposed or unexposed to Salmonella, were sorted into a 96-well plate and processed using scDual-Seq at the four indicated time-points. b tSNE plot of single cells (perplexity = 10) computed based on correlation matrix between single cells using 457 mouse genes with high expression variation (mean/median > 1) and maximum expression higher than 10 tpm. The color indicates exposed (green), unexposed (gray), and induced (black circle). DBscan was used to cluster the cells into two groups. c Boxplot of expression levels (log₁₀ tpm) of the indicated mouse genes across the non-infected, partial-induced, and induced single cells (P < 0.02, Wilcoxon rank sum test). d Boxplots of the sum expression of the previously reported infection gene module [3] across the exposed and unexposed individual cells in our scDual-Seq data (P < 0.0001, Wilcoxon rank sum test). e tSNE plot of single cells (perplexity = 10) computed based on the normalized expression of the previously reported infection gene module [3]. Cells were colored according to their annotation in (a)